"Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version of libxml2.")
endif()
-########################################################################
-# Generate development version info for cache
-########################################################################
-# set(GEN_VERSION_INFO_INTERNAL "ON")
-# include(gmxGenerateVersionString)
-
+ if(GMX_USE_TNG AND NOT GMX_EXTERNAL_TNG)
+ # TNG wants zlib if it is available
+ find_package(ZLIB QUIET)
+ include(gmxTestZLib)
+ gmx_test_zlib(HAVE_ZLIB)
+ endif()
+
########################################################################
# Our own GROMACS tests
########################################################################
message(STATUS "Detecting best SIMD instructions for this CPU")
# Get CPU SIMD properties information
- set(_compile_definitions "@GCC_INLINE_ASM_DEFINE@ -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUID_STANDALONE")
- set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders -DGMX_CPUID_STANDALONE")
++ set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUID_STANDALONE")
if(GMX_TARGET_X86)
set(_compile_definitions "${_compile_definitions} -DGMX_TARGET_X86")
endif()
if(NOT CMAKE_CROSSCOMPILING)
# Get CPU information, e.g. for deciding what SIMD support exists
- set(_compile_definitions "@GCC_INLINE_ASM_DEFINE@ -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUID_STANDALONE")
- set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders -DGMX_CPUID_STANDALONE")
++ set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUID_STANDALONE")
if(GMX_TARGET_X86)
set(_compile_definitions "${_compile_definitions} -DGMX_TARGET_X86")
endif()
#include "xtcio.h"
#include "tngio.h"
#include "trajectory_writing.h"
-#include "checkpoint.h"
-#include "copyrite.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+ #include "gromacs/timing/wallcycle.h"
struct gmx_mdoutf {
t_fileio *fp_trn;
#include "../legacyheaders/types/inputrec.h"
#include "../legacyheaders/types/oenv.h"
#include "../legacyheaders/network.h"
+
+#include "../math/vectypes.h"
++#include "../timing/wallcycle.h"
+#include "../utility/basedefinitions.h"
#include "filenm.h"
#include "enxio.h"
int mdrun_flags,
const t_commrec *cr,
const t_inputrec *ir,
- gmx_mtop_t *mtop,
+ struct gmx_mtop_t *mtop,
- const output_env_t oenv);
+ const output_env_t oenv,
+ gmx_wallcycle_t wcycle);
/*! \brief Getter for file pointer */
FILE *mdoutf_get_fp_field(gmx_mdoutf_t of);
return oenv->xvg_format;
}
-const char *output_env_get_program_name(const output_env_t oenv)
+const char *output_env_get_program_display_name(const output_env_t oenv)
{
- const char *programName = NULL;
++ const char *displayName = NULL;
+
try
{
- return oenv->programContext.displayName();
- programName = oenv->programContext.fullBinaryPath();
++ displayName = oenv->programContext.displayName();
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- return programName;
+
++ return displayName;
}
-const char *output_env_get_short_program_name(const output_env_t oenv)
+const gmx::ProgramContextInterface &
+output_env_get_program_context(const output_env_t oenv)
{
- const char *programName = NULL;
-
- try
- {
- // TODO: Use the display name once it doesn't break anything.
- programName = oenv->programContext.programName();
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
-
- return programName;
-}
-
-const char *output_env_get_cmd_line(const output_env_t oenv)
-{
- const char *commandLine = NULL;
-
- try
- {
- commandLine = oenv->programContext.commandLine();
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
-
- return commandLine;
+ return oenv->programContext;
}
gmx_mdoutf_t *outf, t_mdebin **mdebin,
tensor force_vir, tensor shake_vir,
rvec mu_tot,
- gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags);
+ gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
+ gmx_wallcycle_t wcycle);
/* Routine in sim_util.c */
+gmx_bool use_GPU(const struct nonbonded_verlet_t *nbv);
+
#ifdef __cplusplus
}
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "basenetwork.h"
+
+#include "config.h"
+
+#include <cctype>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
+#include <exception>
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/programcontext.h"
+
+int gmx_gethostname(char *name, size_t len)
+{
+ if (len < 8)
+ {
+ gmx_incons("gmx_gethostname called with len<8");
+ }
+#if defined(HAVE_UNISTD_H) && !defined(__native_client__)
+ if (gethostname(name, len-1) != 0)
+ {
+ std::strncpy(name, "unknown", 8);
+ return -1;
+ }
+ return 0;
+#else
+ std::strncpy(name, "unknown", 8);
+ return -1;
+#endif
+}
+
+gmx_bool gmx_mpi_initialized(void)
+{
+#ifndef GMX_MPI
+ return 0;
+#else
+ int n;
+ MPI_Initialized(&n);
+
+ return n;
+#endif
+}
+
+int gmx_node_num(void)
+{
+#ifndef GMX_MPI
+ return 1;
+#else
+#ifdef GMX_THREAD_MPI
+ if (!gmx_mpi_initialized())
+ {
+ return 1;
+ }
+#endif
+ int i;
+ (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
+ return i;
+#endif
+}
+
+int gmx_node_rank(void)
+{
+#ifndef GMX_MPI
+ return 0;
+#else
+#ifdef GMX_THREAD_MPI
+ if (!gmx_mpi_initialized())
+ {
+ return 0;
+ }
+#endif
+ int i;
+ (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
+ return i;
+#endif
+}
+
+static int mpi_hostname_hash(void)
+{
+ int hash_int;
+
+#ifndef GMX_LIB_MPI
+ /* We have a single physical node */
+ hash_int = 0;
+#else
+ int resultlen;
+ char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
+
+ /* This procedure can only differentiate nodes with different names.
+ * Architectures where different physical nodes have identical names,
+ * such as IBM Blue Gene, should use an architecture specific solution.
+ */
+ MPI_Get_processor_name(mpi_hostname, &resultlen);
+
+ /* The string hash function returns an unsigned int. We cast to an int.
+ * Negative numbers are converted to positive by setting the sign bit to 0.
+ * This makes the hash one bit smaller.
+ * A 63-bit hash (with 64-bit int) should be enough for unique node hashes,
+ * even on a million node machine. 31 bits might not be enough though!
+ */
+ hash_int =
+ (int)gmx_string_fullhash_func(mpi_hostname, gmx_string_hash_init);
+ if (hash_int < 0)
+ {
+ hash_int -= INT_MIN;
+ }
+#endif
+
+ return hash_int;
+}
+
+#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
++#ifdef __clang__
++/* IBM's declaration of this function in
++ * /bgsys/drivers/V1R2M2/ppc64/spi/include/kernel/process.h
++ * erroneously fails to specify __INLINE__, despite
++ * /bgsys/drivers/V1R2M2/ppc64/spi/include/kernel/cnk/process_impl.h
++ * specifiying __INLINE__, so bgclang thinks they are different enough
++ * to complain about. */
++static uint64_t Kernel_GetJobID();
++#endif
+#include <spi/include/kernel/location.h>
+
+static int bgq_nodenum(void)
+{
+ int hostnum;
+ Personality_t personality;
+ Kernel_GetPersonality(&personality, sizeof(personality));
+ /* Each MPI rank has a unique coordinate in a 6-dimensional space
+ (A,B,C,D,E,T), with dimensions A-E corresponding to different
+ physical nodes, and T within each node. Each node has sixteen
+ physical cores, each of which can have up to four hardware
+ threads, so 0 <= T <= 63 (but the maximum value of T depends on
+ the confituration of ranks and OpenMP threads per
+ node). However, T is irrelevant for computing a suitable return
+ value for gmx_hostname_num().
+ */
+ hostnum = personality.Network_Config.Acoord;
+ hostnum *= personality.Network_Config.Bnodes;
+ hostnum += personality.Network_Config.Bcoord;
+ hostnum *= personality.Network_Config.Cnodes;
+ hostnum += personality.Network_Config.Ccoord;
+ hostnum *= personality.Network_Config.Dnodes;
+ hostnum += personality.Network_Config.Dcoord;
+ hostnum *= personality.Network_Config.Enodes;
+ hostnum += personality.Network_Config.Ecoord;
+
+ if (debug)
+ {
+ std::fprintf(debug,
+ "Torus ID A: %d / %d B: %d / %d C: %d / %d D: %d / %d E: %d / %d\n"
+ "Node ID T: %d / %d core: %d / %d hardware thread: %d / %d\n",
+ personality.Network_Config.Acoord,
+ personality.Network_Config.Anodes,
+ personality.Network_Config.Bcoord,
+ personality.Network_Config.Bnodes,
+ personality.Network_Config.Ccoord,
+ personality.Network_Config.Cnodes,
+ personality.Network_Config.Dcoord,
+ personality.Network_Config.Dnodes,
+ personality.Network_Config.Ecoord,
+ personality.Network_Config.Enodes,
+ Kernel_ProcessorCoreID(),
+ 16,
+ Kernel_ProcessorID(),
+ 64,
+ Kernel_ProcessorThreadID(),
+ 4);
+ }
+ return hostnum;
+}
+#endif
+
+int gmx_physicalnode_id_hash(void)
+{
+ int hash;
+
+#ifndef GMX_MPI
+ hash = 0;
+#else
+#ifdef GMX_THREAD_MPI
+ /* thread-MPI currently puts the thread number in the process name,
+ * we might want to change this, as this is inconsistent with what
+ * most MPI implementations would do when running on a single node.
+ */
+ hash = 0;
+#else
+#ifdef GMX_TARGET_BGQ
+ hash = bgq_nodenum();
+#else
+ hash = mpi_hostname_hash();
+#endif
+#endif
+#endif
+
+ if (debug)
+ {
+ fprintf(debug, "In gmx_physicalnode_id_hash: hash %d\n", hash);
+ }
+
+ return hash;
+}
+
+#ifdef GMX_LIB_MPI
+void gmx_abort(int errorno)
+{
+ const char *programName = "GROMACS";
+ try
+ {
+ programName = gmx::getProgramContext().displayName();
+ }
+ catch (const std::exception &)
+ {
+ }
+ const int nnodes = gmx_node_num();
+ const int noderank = gmx_node_rank();
+ if (nnodes > 1)
+ {
+ std::fprintf(stderr, "Halting parallel program %s on rank %d out of %d\n",
+ programName, noderank, nnodes);
+ }
+ else
+ {
+ std::fprintf(stderr, "Halting program %s\n", programName);
+ }
+
+ MPI_Abort(MPI_COMM_WORLD, errorno);
+ std::exit(errorno);
+}
+#endif
--- /dev/null
- #define GMX_MPI_REAL MPI_DOUBLE
- #define GMX_REAL_EPS GMX_DOUBLE_EPS
- #define GMX_REAL_MIN GMX_DOUBLE_MIN
- #define GMX_REAL_MAX GMX_DOUBLE_MAX
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares `real` and related constants.
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_REAL_H
+#define GMX_UTILITY_REAL_H
+
+/*! \brief Double precision accuracy */
+#define GMX_DOUBLE_EPS 2.2204460492503131e-16
+
+/*! \brief Maximum double precision value - reduced 1 unit in last digit for MSVC */
+#define GMX_DOUBLE_MAX 1.7976931348623157e+308
+
+/*! \brief Minimum double precision value */
+#define GMX_DOUBLE_MIN 2.2250738585072014e-308
+
+/*! \brief Single precision accuracy */
+#define GMX_FLOAT_EPS 1.19209290e-07F
+
+/*! \brief Maximum single precision value - reduced 1 unit in last digit for MSVC */
+#define GMX_FLOAT_MAX 3.40282346E+38F
+
+/*! \brief Minimum single precision value */
+#define GMX_FLOAT_MIN 1.175494351E-38F
+
++#ifdef __PGI
++/* The portland group x86 C/C++ compilers do not treat negative zero initializers
++ * correctly, but "optimizes" them to positive zero, so we implement it explicitly.
++ * These constructs are optimized to simple loads at compile time. If you want to
++ * use them on other compilers those have to support gcc preprocessor extensions.
++ * Note: These initializers might be sensitive to the endianness (which can
++ * be different for byte and word order), so check that it works for your platform
++ * and add a separate section if necessary before adding to the ifdef above.
++ */
++# define GMX_DOUBLE_NEGZERO ({ const union { int di[2]; double d; } _gmx_dzero = {0, -2147483648}; _gmx_dzero.d; })
++# define GMX_FLOAT_NEGZERO ({ const union { int fi; float f; } _gmx_fzero = {-2147483648}; _gmx_fzero.f; })
++#else
++/*! \brief Negative zero in double */
++# define GMX_DOUBLE_NEGZERO (-0.0)
++
++/*! \brief Negative zero in float */
++# define GMX_FLOAT_NEGZERO (-0.0f)
++#endif
+
+/*! \typedef real
+ * \brief Precision-dependent \Gromacs floating-point type.
+ */
+/*! \def HAVE_REAL
+ * \brief Used to check whether `real` is already defined.
+ */
+/*! \def GMX_MPI_REAL
+ * \brief MPI data type for `real`.
+ */
+/*! \def GMX_REAL_EPS
+ * \brief Accuracy for `real`.
+ */
+/*! \def GMX_REAL_MIN
+ * \brief Smallest non-zero value for `real`.
+ */
+/*! \def GMX_REAL_MAX
+ * \brief Largest finite value for `real`.
+ */
++/*! \def GMX_REAL_NEGZERO
++ * \brief Negative zero for `real`.
++ */
+/*! \def gmx_real_fullprecision_pfmt
+ * \brief Format string for full `real` precision.
+ */
+#ifdef GMX_DOUBLE
+
+#ifndef HAVE_REAL
+typedef double real;
+#define HAVE_REAL
+#endif
+
- #define GMX_MPI_REAL MPI_FLOAT
- #define GMX_REAL_EPS GMX_FLOAT_EPS
- #define GMX_REAL_MIN GMX_FLOAT_MIN
- #define GMX_REAL_MAX GMX_FLOAT_MAX
++#define GMX_MPI_REAL MPI_DOUBLE
++#define GMX_REAL_EPS GMX_DOUBLE_EPS
++#define GMX_REAL_MIN GMX_DOUBLE_MIN
++#define GMX_REAL_MAX GMX_DOUBLE_MAX
++#define GMX_REAL_NEGZERO GMX_DOUBLE_NEGZERO
+#define gmx_real_fullprecision_pfmt "%21.14e"
+
+#else /* GMX_DOUBLE */
+
+#ifndef HAVE_REAL
+typedef float real;
+#define HAVE_REAL
+#endif
+
++#define GMX_MPI_REAL MPI_FLOAT
++#define GMX_REAL_EPS GMX_FLOAT_EPS
++#define GMX_REAL_MIN GMX_FLOAT_MIN
++#define GMX_REAL_MAX GMX_FLOAT_MAX
++#define GMX_REAL_NEGZERO GMX_FLOAT_NEGZERO
+#define gmx_real_fullprecision_pfmt "%14.7e"
+
+#endif /* GMX_DOUBLE */
+
+#endif
#include <dmalloc.h>
#endif
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "thread_mpi/threads.h"
+#include "gromacs/utility/fatalerror.h"
#ifdef PRINT_ALLOC_KB
-#include "gromacs/legacyheaders/network.h"
++#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/gmxmpi.h"
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff